Symlinks
Symlinks are like shortcuts, except they let us reorganize files without breaking dependent applications.

The Problem
In the past, browsing into the EverQuest root folder caused my Windows file explorer to hang momentarily. That's because there's so many darn files in that folder. So to fix that, I'm creating a new root folder for the game, and only putting files and folders that I commonly access there.
The first step of this process is to move the location of the game folder. It's a little cleaner to install the game to this new path (your uninstallers would still work then), but that probably isn't convenient for most people reading this. No big deal.

We just created a new root folder "EQ" and relocated the old root to it. Then we linked the "uifiles" folder in our new root, so that the game knows where the folder is now located. I can move files similarly, omitting the /J parameter which is just for directories. Also make sure to open the command prompt as administrator for this:

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Now I'll link some files and folders that I want to see in my new root:

There, that should narrow things down a bit for us. Here's how my EQ folder looks now:

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Finally, make sure the game shortcut points the new location of LaunchPad.exe.
Full disclosure: to be perfectly honest, this problem doesn't affect me anymore since I use a solid state drive. However I still wanted to do it to placate my ocd.
Your mileage may vary. Use at your own risk.